Phils most awesome workflow 8 23 2022 change

Packages

library(readr)

Warning: package ‘readr’ was built under R version 4.0.5

library(dplyr)

Warning: package ‘dplyr’ was built under R version 4.0.5
Attaching package: ‘dplyr’

The following objects are masked from ‘package:stats’:

    filter, lag

The following objects are masked from ‘package:base’:

    intersect, setdiff, setequal, union

library(ggplot2)

Warning: package ‘ggplot2’ was built under R version 4.0.5

library(plotly)

Warning: package ‘plotly’ was built under R version 4.0.5Registered S3 method overwritten by 'data.table':
  method           from
  print.data.table     
Registered S3 methods overwritten by 'htmltools':
  method               from         
  print.html           tools:rstudio
  print.shiny.tag      tools:rstudio
  print.shiny.tag.list tools:rstudio
Registered S3 method overwritten by 'htmlwidgets':
  method           from         
  print.htmlwidget tools:rstudio

Attaching package: ‘plotly’

The following object is masked from ‘package:ggplot2’:

    last_plot

The following object is masked from ‘package:stats’:

    filter

The following object is masked from ‘package:graphics’:

    layout

load data

X35020903 <- read_csv("https://ndownloader.figshare.com/files/35020903")

Rows: 1840 Columns: 29── Column specification ────────────────────────────────────────────────────────
Delimiter: ","
chr (27): DepMap_ID, cell_line_name, stripped_cell_line_name, CCLE_Name, ali...
dbl  (2): COSMICID, WTSI_Master_Cell_ID
ℹ Use `spec()` to retrieve the full column specification for this data.
ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.

X35020903

wrangle data

edit_x35 <- X35020903 %>%
 filter(sex %in% "Female" | is.na(sex)) %>%
 filter(!(lineage %in% "unknown"))

viz data

dv1 <- ggplot(edit_x35) +
 aes(x = primary_disease, fill = lineage) +
 geom_bar() +
 scale_fill_hue(direction = 1) +
 coord_flip() +
 theme_minimal()

dv1

ggplotly(dv1)